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- PDB-1nhz: Crystal Structure of the Antagonist Form of Glucocorticoid Receptor -

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Entry
Database: PDB / ID: 1nhz
TitleCrystal Structure of the Antagonist Form of Glucocorticoid Receptor
ComponentsGLUCOCORTICOID RECEPTOR
KeywordsHormone receptor / PROTEIN-LIGAND COMPLEX / ANTI PARALLEL ALPHA HELIX SANDWICH
Function / homology
Function and homology information


Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / PTK6 Expression / neuroinflammatory response / glucocorticoid metabolic process / microglia differentiation / mammary gland duct morphogenesis / maternal behavior ...Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / PTK6 Expression / neuroinflammatory response / glucocorticoid metabolic process / microglia differentiation / mammary gland duct morphogenesis / maternal behavior / astrocyte differentiation / cellular response to glucocorticoid stimulus / motor behavior / regulation of gluconeogenesis / adrenal gland development / cellular response to steroid hormone stimulus / estrogen response element binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / intracellular steroid hormone receptor signaling pathway / core promoter sequence-specific DNA binding / cellular response to transforming growth factor beta stimulus / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / TBP-class protein binding / steroid binding / cellular response to dexamethasone stimulus / synaptic transmission, glutamatergic / chromosome segregation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hsp90 protein binding / SUMOylation of intracellular receptors / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / Nuclear Receptor transcription pathway / spindle / Regulation of RUNX2 expression and activity / nuclear receptor activity / positive regulation of neuron apoptotic process / sequence-specific double-stranded DNA binding / Circadian Clock / chromatin organization / gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / Potential therapeutics for SARS / DNA-binding transcription factor activity, RNA polymerase II-specific / mitochondrial matrix / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / cell division / negative regulation of DNA-templated transcription / centrosome / apoptotic process / synapse / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / zinc ion binding / nucleoplasm / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Glucocorticoid receptor / Glucocorticoid receptor / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors ...Glucocorticoid receptor / Glucocorticoid receptor / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-486 / HEXANE-1,6-DIOL / Glucocorticoid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKauppi, B. / Jakob, C. / Farnegardh, M. / Yang, J. / Ahola, H. / Alarcon, M. / Calles, K. / Engstrom, O. / Harlan, J. / Muchmore, S. ...Kauppi, B. / Jakob, C. / Farnegardh, M. / Yang, J. / Ahola, H. / Alarcon, M. / Calles, K. / Engstrom, O. / Harlan, J. / Muchmore, S. / Ramqvist, A.-K. / Thorell, S. / Ohman, L. / Greer, J. / Gustafsson, J.-A. / Carlstedt-Duke, J. / Carlquist, M.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: The Three-dimensional Structures of Antagonistic and Agonistic Forms of the Glucocorticoid Receptor Ligand-binding Domain: RU-486 INDUCES A TRANSCONFORMATION THAT LEADS TO ACTIVE ANTAGONISM.
Authors: Kauppi, B. / Jakob, C. / Farnegardh, M. / Yang, J. / Ahola, H. / Alarcon, M. / Calles, K. / Engstrom, O. / Harlan, J. / Muchmore, S. / Ramqvist, A.-K. / Thorell, S. / Ohman, L. / Greer, J. / ...Authors: Kauppi, B. / Jakob, C. / Farnegardh, M. / Yang, J. / Ahola, H. / Alarcon, M. / Calles, K. / Engstrom, O. / Harlan, J. / Muchmore, S. / Ramqvist, A.-K. / Thorell, S. / Ohman, L. / Greer, J. / Gustafsson, J.-A. / Carlstedt-Duke, J. / Carlquist, M.
History
DepositionDec 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Sep 2, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / struct_keywords ...chem_comp / struct_keywords / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _struct_keywords.text ..._chem_comp.pdbx_synonyms / _struct_keywords.text / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUCOCORTICOID RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9395
Polymers32,1551
Non-polymers7844
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: GLUCOCORTICOID RECEPTOR
hetero molecules

A: GLUCOCORTICOID RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,87810
Polymers64,3102
Non-polymers1,5688
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7050 Å2
ΔGint-4 kcal/mol
Surface area23400 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)74.859, 109.764, 39.261
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-95-

HOH

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Components

#1: Protein GLUCOCORTICOID RECEPTOR / / GR


Mass: 32155.072 Da / Num. of mol.: 1
Fragment: residue 500-777, hinge and steroid binding domains
Mutation: N517D, F602S, C638D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P04150
#2: Chemical ChemComp-486 / 11-(4-DIMETHYLAMINO-PHENYL)-17-HYDROXY-13-METHYL-17-PROP-1-YNYL-1,2,6,7,8,11,12,13,14,15,16,17-DODEC AHYDRO-CYCLOPENTA[A]PHENANTHREN-3-ONE / RU-486 / MIFEPRISTONE / Mifepristone


Mass: 429.594 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H35NO2 / Comment: medication*YM
#3: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL / 1,6-Hexanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: PEG 8000, 1, 6-hexanediol, NaSCN, Tris-HCl, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal grow
*PLUS
Temperature: 12 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115 %PEG80001reservoir
2900 mM1,6-hexanediol1reservoir
3600 mM1reservoirNaSCN
4100 mMTris-HCl1reservoirpH8.2
510 mMTris-HCl1droppH8.5
62.5 mMdithiothreitol1drop
750000 nMRU-4861drop
85-12 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 26, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.3→39.26 Å / Num. all: 14833 / Num. obs: 14815 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.035 / Net I/σ(I): 8.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.141 / Mean I/σ(I) obs: 6.1 / Num. unique all: 2064 / Rsym value: 0.121 / % possible all: 99.1
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 40 Å / % possible obs: 98.1 % / Rmerge(I) obs: 0.106
Reflection shell
*PLUS
% possible obs: 98 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMAC5.1.19refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→62.02 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.881 / SU B: 6.11 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.299 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27585 743 5 %RANDOM
Rwork0.2044 ---
all0.20787 14815 --
obs0.20787 14072 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.433 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--2.84 Å20 Å2
3----2.89 Å2
Refinement stepCycle: LAST / Resolution: 2.3→62.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 56 128 2136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222050
X-RAY DIFFRACTIONr_bond_other_d0.0030.021903
X-RAY DIFFRACTIONr_angle_refined_deg1.7971.9922767
X-RAY DIFFRACTIONr_angle_other_deg2.36334441
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0835237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.110.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022174
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02412
X-RAY DIFFRACTIONr_nbd_refined0.230.2487
X-RAY DIFFRACTIONr_nbd_other0.2320.22221
X-RAY DIFFRACTIONr_nbtor_other0.1050.21230
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2103
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2680.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2340.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2690.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7971.51193
X-RAY DIFFRACTIONr_mcangle_it1.53821931
X-RAY DIFFRACTIONr_scbond_it2.5013857
X-RAY DIFFRACTIONr_scangle_it4.044.5836
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.251 64
Rwork0.196 1002
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 40 Å / Rfactor Rfree: 0.263 / Rfactor Rwork: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.36 Å

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